Hi Jacob,
If you have a sufficient number of unique reflections, use percentage
because it is more convenient. If not, at least make sure the below
criteria are met. If that's not possible, don't use maximum likelihood
for refinement ;-)
Cheers,
Tim
On 11/21/2014 05:09 PM, Keller, Jacob wrote:
> Agree with all of this—but how does it reflect on the original question of whether to use a percent or an absolute number?
>
> JPK
>
> From: Pavel Afonine [mailto:[log in to unmask]]
> Sent: Friday, November 21, 2014 11:02 AM
> To: Keller, Jacob
> Cc: [log in to unmask]
> Subject: Re: [ccp4bb] Free Reflections as Percent and not a Number
>
> Hello,
>
> choice of the size of free (or test, whatever you like to call them) reflections is important for three different purposes:
>
> - estimation of parameters for ML target for refinement;
> - map calculation (coefficients m&D in 2mFo-DFc or mFo-DFc map are calculated using test reflections);
> - validation (calculation Rfree).
>
> It is important that free reflections are evenly distributed across the whole resolution range, and each sufficiently thin resolution bin contains at least 50 test reflections so that the estimation of ML parameters is robust and reliable. "Sufficiently thin resolution bin" is such that ML parameters can be assumed constants in it.
>
> Smaller test sets will result in less stable refinements (refinement outcome will strongly depend on the choice of test set).
>
> Larger test sets will damage map quality (unless all reflections are used in map calculation).
>
> Size of free set needs to be sufficiently large so that Rfree is statistically meaningful.
>
> Nothing new is said above, it's all documented in the literature!
>
> Pavel
>
>
> On Thu, Nov 20, 2014 at 2:43 PM, Keller, Jacob <[log in to unmask]<mailto:[log in to unmask]>> wrote:
> Dear Crystallographers,
>
> I thought that for reliable values for Rfree, one needs only to satisfy counting statistics, and therefore using at most a couple thousand reflections should always be sufficient. Almost always, however, some seemingly-arbitrary percentage of reflections is used, say 5%. Is there any rationale for using a percentage rather than some absolute number like 1000?
>
> All the best,
>
> Jacob
>
--
Dr Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
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